Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity.Using de novo long-read assembly,we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.Our pan-genome reveals extensive structural variations(SVs)and gene presence/absence variations.Additionally,our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter-and intraspecific diversity.Moreover,we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes.We characterized genetic variants associated with submergence tolerance,seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice.This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

Lianguang Shang;Xiaoxia Li;Huiying He;Qiaoling Yuan;Yanni Song;Zhaoran Wei;Hai Lin;Min Hu;Fengli Zhao;Chao Zhang;Yuhua Li;Hongsheng Gao;Tianyi Wang;Xiangpei Liu;Hong Zhang;Ya Zhang;Shuaimin Cao;Xiaoman Yu;Bintao Zhang;Yong Zhang;Yiqing Tan;Mao Qin;Cheng Ai;Yingxue Yang;Bin Zhang;Zhiqiang Hu;Hongru Wang;Yang Lv;Yuexing Wang;Jie Ma;Quan Wang;Hongwei Lu;Zhe Wu;Shanlin Liu;Zongyi Sun;Hongliang Zhang;Longbiao Guo;Zichao Li;Yongfeng Zhou;Jiayang Li;Zuofeng Zhu;Guosheng Xiong;Jue Ruan;Qian Qian

Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,Guangdong,China;State Key Laboratory for Agrobiotechnology,National Center for Evaluation of Agricultural Wild Plants(Rice),Department of Plant Genetics and Breeding,China Agricultural University,Beijing,China;Academy for Advanced Interdisciplinary Studies,Plant Phenomics Research Center,Nanjing Agricultural University,Nanjing,Jiangsu,China;Department of Plant and Microbial Biology,University of California,Berkeley,Berkeley,CA,USA;Department of Integrative Biology,University of California,Berkeley,Berkeley,CA,USA;State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou,Zhejiang,China;Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes,Institute of Plant and Food Science,Department of Biology,School of Life Sciences,Southern University of Science and Technology,Shenzhen,Guangdong,China;Department of Entomology,College of Plant Protection,China Agricultural University,Beijing,China;Grandomics Biosciences,Beijing,China;State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement,College of Agronomy and Biotechnology,China Agricultural University,Beijing,China;State Key Laboratory of Plant Genomics,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing,China

细胞研究（英文版）

[1]Lianguang Shang;Xiaoxia Li;Huiying He;Qiaoling Yuan;Yanni Song;Zhaoran Wei;Hai Lin;Min Hu;Fengli Zhao;Chao Zhang;Yuhua Li;Hongsheng Gao;Tianyi Wang;Xiangpei Liu;Hong Zhang;Ya Zhang;Shuaimin Cao;Xiaoman Yu;Bintao Zhang;Yong Zhang;Yiqing Tan;Mao Qin;Cheng Ai;Yingxue Yang;Bin Zhang;Zhiqiang Hu;Hongru Wang;Yang Lv;Yuexing Wang;Jie Ma;Quan Wang;Hongwei Lu;Zhe Wu;Shanlin Liu;Zongyi Sun;Hongliang Zhang;Longbiao Guo;Zichao Li;Yongfeng Zhou;Jiayang Li;Zuofeng Zhu;Guosheng Xiong;Jue Ruan;Qian Qian-.A super pan-genomic landscape of rice)[J].细胞研究（英文版）,2022(10):878-896

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